The solution which I got to work (for posterity) was to modify the grammar
to accept my comment tags as modifiers. I'm then browsing the AST and
manually
outputting the requisite code (advantage is simplicity and precise control
over handling of indenting, comments, etc).

I took a look at the JavaFront tool and StrategoXT. They look excellent
for performing global code cleanups and project-specific lint checks
in the future, similar to what the DMS can do (from my reading).